Natural selection and repeated patterns of molecular evolution following allopatric divergence
- North Carolina State University, United States
- University of Florida, United States
- Beijing Genomics Institute, China
- Chinese Academy of Sciences, China
- Zhejiang University, China
Abstract
Although geographic isolation is a leading driver of speciation, the tempo and pattern of divergence at the genomic level remain unclear. We examine genome-wide divergence of putatively single-copy orthologous genes (POGs) in 20 allopatric species/variety pairs from diverse angiosperm clades, with 16 pairs reflecting the classic eastern Asia-eastern North America floristic disjunction. In each pair, >90% of POGs are under purifying selection, and <10% are under positive selection. A set of POGs are under strong positive selection, 14 of which are shared by 10-15 pairs, and one shared by all pairs; 15 POGs are annotated to biological processes responding to various stimuli. The relative abundance of POGs under different selective forces exhibits a repeated pattern among pairs despite an ~10-million-year difference in divergence time. Species divergence times are positively correlated with abundance of POGs under moderate purifying selection, but negatively correlated with abundance of POGs under strong purifying selection.
Data availability
Sequences of ortologous gene families and pairs of POGs sequences used for calculation of Ka and Ks have been submitted to Dryad (https://datadryad.org//). Raw transcriptome data have been submitted to NCBI SRA database with Bioproject number PRJNA508825 and Biosample number from SAMN10534244 to SAMN10534283 (Supplementary File 11).
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Natural selection and repeated patterns of molecular evolution following allopatric divergenceBioproject number PRJNA508825 and Biosample number from SAMN10534244 to SAMN10534283.
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Data from: Natural selection and repeated genome-wide patterns of molecular evolution following allopatric divergenceDryad Digital Repository, 10.5061/dryad.f1f0q44.
Article and author information
Author details
Funding
National Science Foundation (DEB-442161)
- Yibo Dong
- Wenbin Zhou
- Jenny Xiang
National Science Foundation (DEB-442280)
- Shichao Chen
- Pamela S Soltis
- Douglas E Soltis
National Science Foundation of China (IOS-024629)
- Shichao Chen
- Yun-peng Zhao
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Reviewing Editor
- Daniel J Kliebenstein, University of California, Davis, United States
Publication history
- Received: January 15, 2019
- Accepted: August 1, 2019
- Accepted Manuscript published: August 2, 2019 (version 1)
- Version of Record published: September 13, 2019 (version 2)
- Version of Record updated: September 20, 2019 (version 3)
- Version of Record updated: January 17, 2020 (version 4)
Copyright
© 2019, Dong et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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Natural selection and repeated patterns of molecular evolution following allopatric divergence
eLife 8:e45199.
https://doi.org/10.7554/eLife.45199
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